bold tutorial
for v0.5.0
bold is an R package to connect to BOLD Systems via their API. Functions in bold let you search for sequence data, specimen data, sequence + specimen data, and download raw trace files.
bold info
Installation
You can install the stable version from CRAN
install.packages("bold")
Or the development version from Github
install.packages("devtools")
devtools::install_github("ropensci/bold")
Then load the package into the R sesssion
library("bold")
Usage
Search for taxonomic names via names
bold_tax_name searches for names with names.
bold_tax_name(name = 'Diplura')
#> taxid taxon tax_rank tax_division parentid parentname
#> 1 603673 Diplura genus Protists 53974 Scytosiphonaceae
#> 2 734358 Diplura class Animals 20 Arthropoda
#> specimenrecords taxonrep representitive_image.image
#> 1 6 <NA> <NA>
#> 2 204 Diplura GBARA/GBOL14725+1435775798.jpg
#> representitive_image.apectratio input
#> 1 NA Diplura
#> 2 2.219 Diplura
bold_tax_name(name = c('Diplura', 'Osmia'))
#> taxid taxon tax_rank tax_division parentid parentname
#> 1 603673 Diplura genus Protists 53974 Scytosiphonaceae
#> 2 734358 Diplura class Animals 20 Arthropoda
#> 3 4940 Osmia genus Animals 4962 Megachilinae
#> specimenrecords taxonrep representitive_image.image
#> 1 6 <NA> <NA>
#> 2 204 Diplura GBARA/GBOL14725+1435775798.jpg
#> 3 2172 Osmia BUSA/IMG_3061.jpg
#> representitive_image.apectratio input
#> 1 NA Diplura
#> 2 2.219 Diplura
#> 3 1.486 Osmia
Search for taxonomic names via BOLD identifiers
bold_tax_id searches for names with BOLD identifiers.
bold_tax_id(id = 88899)
#> input taxid taxon tax_rank tax_division parentid parentname
#> 1 88899 88899 Momotus genus Animals 88898 Momotidae
bold_tax_id(id = c(88899, 125295))
#> input taxid taxon tax_rank tax_division parentid parentname
#> 1 88899 88899 Momotus genus Animals 88898 Momotidae
#> 2 125295 125295 Helianthus genus Plants 151101 Asteroideae
#> taxonrep
#> 1 <NA>
#> 2 Helianthus
Search for sequence data only
The BOLD sequence API gives back sequence data, with a bit of metadata.
The default is to get a list back
bold_seq(taxon = 'Coelioxys')[1:2]
#> [[1]]
#> [[1]]$id
#> [1] "BBHYL404-10"
#>
#> [[1]]$name
#> [1] "Coelioxys rufitarsis"
#>
#> [[1]]$gene
#> [1] "BBHYL404-10"
#>
#> [[1]]$sequence
#> [1] "TATAATATATATAATTTTTGCAATATGATCAGGTATAATTGGATCATCTTTAAGAATAATTATTCGAATAGAATTAAGAATCCCAGGTTCATGAATTAGAAATGATCAAATTTATAATTCTTTTATTACAGCACATGCATTTTTAATAATTTTTTTTTTAGTTATGCCTTTTCTAATTGGGGGATTTGGTAATTGATTAACACCATTAATACTTGGAGCTCCTGATATAGCTTTCCCCCGAATAAACAATATTAGATTTTGACTACTCCCACCTTCTTTATTACTTTTATTATCAAGAAATTTAATTAATCCAAGACCAGGAACAGGATGAACTGTTTATCCACCATTATCCTCTTATACATATCATCCATCTCCTTCTGTAGATTTAGCAATTTTTTCTTTACATTTATCAGGAATTTCCTCAATTATTGGATCAATAAATTTTATTGTTACAATTTTAATAATAAAAAATTATTCAATAAATTATAATCAAATACCATTATTCCCATGATCAGTTTTAATTACTACAATTTTATTATTACTATCACTTCCAGTATTAGCAGGAGCAATTACAATATTATTATTTGATCGAAATTTAAATTCTTCTTTTTTTGACCCAATAGGAGGAGGAGACCCAATTTTATATCAACATTTATTT\r"
#>
#>
#> [[2]]
#> [[2]]$id
#> [1] "BCT004-06"
#>
#> [[2]]$name
#> [1] "Coelioxys modesta"
#>
#> [[2]]$gene
#> [1] "BCT004-06"
#>
#> [[2]]$sequence
#> [1] "-ATATTATATATAATTTTTGCAATATGATCAGGTATAATTGGATCATCTTTAAGAATAATTATTCGCATAGAATTAAGAATCCCAGGTTCTTGAATTAACAATGATCAAATTTATAATTCTTTTATTACAGCTCATGCCTTTTTAATAATTTTTTTCCTAGTGATACCCTTTTTAATTGGTGGATTTGGTAATTGATTAGTACCCTTAATAATTGGAGCTCCAGATATAGCCTTTCCACGAATAAATAATATTAGATTTTGACTTTTACCCCCTTCTTTATTACTTTTATTATCAAGAAATTTAATTAATCCTAGACCTGGTACCGGATGAACAGTTTACCCACCTTTATCTTTATATAATTTTCATCCTTCTCCTTCAGTTGATTTAGCTATTTTTTCATTACATTTATCTGGAATTTCATCTATTATTGGATCAATAAATTTTATTGTTACTATTTTAATAATAAAAAATTTTTCATTAAATTATAGACAAATACCTTTATTTCCATGATCAGTTATAATTACTACAATCTTATTATTATTATCTTTACCAGTATTAGCAGGAGCAATCACAATATTATTATTTGATCGAAATTTTAATTCTTCATTTTTTGACCCTATAGGAGGAGGAGACCCAATTTTATATCAACACTTATTT\r"
You can optionally get back the httr response object
res <- bold_seq(taxon = 'Coelioxys', response = TRUE)
res$headers
#> NULL
You can do geographic searches
bold_seq(geo = "USA")
#> [[1]]
#> [[1]]$id
#> [1] "GBAN1777-08"
#>
#> [[1]]$name
#> [1] "Macrobdella decora"
#>
#> [[1]]$gene
#> [1] "GBAN1777-08"
#>
#> [[1]]$sequence
#> [1] "---------------------------------ATTGGAATCTTGTATTTCTTATTAGGTACATGATCTGCTATAGTAGGGACCTCTATA---AGAATAATTATTCGAATTGAATTAGCTCAACCTGGGTCGTTTTTAGGAAAT---GATCAAATTTACAATACTATTGTTACTGCTCATGGATTAATTATAATTTTTTTTATAGTAATACCTATTTTAATTGGAGGGTTTGGTAATTGATTAATTCCGCTAATA---ATTGGTTCTCCTGATATAGCTTTTCCACGTCTTAATAATTTAAGATTTTGATTACTTCCGCCATCTTTAACTATACTTTTTTGTTCATCTATAGTCGAAAATGGAGTAGGTACTGGATGGACTATTTACCCTCCTTTAGCAGATAACATTGCTCATTCTGGACCTTCTGTAGATATA---GCAATTTTTTCACTTCATTTAGCTGGTGCTTCTTCTATTTTAGGTTCATTAAATTTTATTACTACTGTAGTTAATATACGATGACCAGGGATATCTATAGAGCGAATTCCTTTATTTATTTGATCCGTAATTATTACTACTGTATTGCTATTATTATCTTTACCAGTATTAGCAGCT---GCTATTTCAATATTATTAACAGATCGTAACTTAAATACTAGATTTTTTGACCCAATAGGAGGAGGGGATCCTATTTTATTCCAACATTTATTTTGATTTTTTGGCCACCCTGAAGTTTATATTTTAATTTTACCAGGATTTGGAGCTATTTCTCATGTAGTAAGTCATAACTCT---AAAAAATTAGAACCGTTTGGATCATTAGGGATATTATATGCAATAATTGGAATTGCAATTTTAGGTTTTATTGTTTGAGCACATCATATATTTACAGTAGGTCTTGATGTAGATACACGAGCTTATTTTACAGCAGCTACAATAGTTATTGCTGTTCCTACAGGAATTAAAGTATTTAGGTGATTG---GCAACT\r"
#>
#>
#> [[2]]
#> [[2]]$id
#> [1] "GBAN1780-08"
#>
#> [[2]]$name
#> [1] "Haemopis terrestris"
#>
#> [[2]]$gene
#> [1] "GBAN1780-08"
#>
#> [[2]]$sequence
#> [1] "---------------------------------ATTGGAACWTTWTATTTTATTTTNGGNGCTTGATCTGCTATATTNGGGATCTCAATA---AGGAATATTATTCGAATTGAGCCATCTCAACCTGGGAGATTATTAGGAAAT---GATCAATTATATAATTCATTAGTAACAGCTCATGGATTAATTATAATTTTCTTTATGGTTATGCCTATTTTGATTGGTGGGTTTGGTAATTGATTACTACCTTTAATA---ATTGGAGCCCCTGATATAGCTTTTCCTCGATTAAATAATTTAAGTTTTTGATTATTACCACCTTCATTAATTATATTGTTAAGATCCTCTATTATTGAAAGAGGGGTAGGTACAGGTTGAACCTTATATCCTCCTTTAGCAGATAGATTATTTCATTCAGGTCCATCGGTAGATATA---GCTATTTTTTCATTACATATAGCTGGAGCATCATCTATTTTAGGCTCATTAAACTTTATTTCTACAATTATTAATATACGAATTAAAGGTATAAGATCTGATCGAGTACCTTTATTTGTATGATCAGTTGTTATTACAACAGTTCTGTTATTATTGTCTTTACCTGTTTTAGCTGCA---GCTATTACTATATTATTAACAGATCGTAATTTAAATACTACTTTTTTTGATCCTATAGGAGGTGGAGATCCAGTATTGTTTCAACACTTATTTTGATTTTTTGGTCATCCAGAAGTATATATTTTGATTTTACCAGGATTTGGAGCAATTTCTCATATTATTACAAATAATTCT---AAAAAATTGGAACCTTTTGGATCTCTTGGTATAATTTATGCTATAATTGGAATTGCAGTTTTAGGGTTTATTGTATGAGCCCATCATATATTTACTGTAGGATTAGATGTTGATACTCGAGCTTATTTTACAGCAGCTACTATAGTTATTGCTGTTCCTACTGGTATTAAAGTTTTTAGGTGATTA---GCAACA\r"
#>
#>
#> [[3]]
#> [[3]]$id
#> [1] "GBNM0293-06"
#>
#> [[3]]$name
#> [1] "Steinernema carpocapsae"
#>
#> [[3]]$gene
#> [1] "GBNM0293-06"
#>
#> [[3]]$sequence
#> [1] "---------------------------------------------------------------------------------ACAAGATTATCTCTTATTATTCGTTTAGAGTTGGCTCAACCTGGTCTTCTTTTGGGTAAT---GGTCAATTATATAATTCTATTATTACTGCTCATGCTATTCTTATAATTTTTTTCATAGTTATACCTAGAATAATTGGTGGTTTTGGTAATTGAATATTACCTTTAATATTGGGGGCTCCTGATATAAGTTTTCCACGTTTGAATAATTTAAGTTTTTGATTGCTACCAACTGCTATATTTTTGATTTTAGATTCTTGTTTTGTTGACACTGGTTGTGGTACTAGTTGAACTGTTTATCCTCCTTTGAGG---ACTTTAGGTCACCCTGGYAGAAGTGTAGATTTAGCTATTTTTAGTCTTCATTGTGCAGGAATTAGCTCAATTTTAGGGGCTATTAATTTTATATGTACTACAAAAAATCTTCGTAGTAGTTCTATTTCTTTGGAACATATAAGACTTTTTGTTTGGGCTGTTTTTGTTACTGTTTTTTTATTAGTTTTATCTTTACCTGTTTTAGCTGGTGCTATTACTATGCTTTTAACAGACCGTAATTTAAATACTTCTTTTTTT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------\r"
#>
#>
#> [[4]]
#> [[4]]$id
#> [1] "NEONV108-11"
#>
#> [[4]]$name
#> [1] "Aedes thelcter"
#>
#> [[4]]$gene
#> [1] "NEONV108-11"
#>
#> [[4]]$sequence
#> [1] "AACTTTATACTTCATCTTCGGAGTTTGATCAGGAATAGTTGGTACATCATTAAGAATTTTAATTCGTGCTGAATTAAGTCAACCAGGTATATTTATTGGAAATGACCAAATTTATAATGTAATTGTTACAGCTCATGCTTTTATTATAATTTTCTTTATAGTTATACCTATTATAATTGGAGGATTTGGAAATTGACTAGTTCCTCTAATATTAGGAGCCCCAGATATAGCTTTCCCTCGAATAAATAATATAAGTTTTTGAATACTACCTCCCTCATTAACTCTTCTACTTTCAAGTAGTATAGTAGAAAATGGATCAGGAACAGGATGAACAGTTTATCCACCTCTTTCATCTGGAACTGCTCATGCAGGAGCCTCTGTTGATTTAACTATTTTTTCTCTTCATTTAGCCGGAGTTTCATCAATTTTAGGGGCTGTAAATTTTATTACTACTGTAATTAATATACGATCTGCAGGAATTACTCTTGATCGACTACCTTTATTCGTTTGATCTGTAGTAATTACAGCTGTTTTATTACTTCTTTCACTTCCTGTATTAGCTGGAGCTATTACAATACTATTAACTGATCGAAATTTAAATACATCTTTCTTTGATCCAATTGGAGGAGGAGACCCAATTTTATACCAACATTTATTT\r"
#>
#>
#> [[5]]
#> [[5]]$id
#> [1] "NEONV109-11"
#>
#> [[5]]$name
#> [1] "Aedes thelcter"
#>
#> [[5]]$gene
#> [1] "NEONV109-11"
#>
#> [[5]]$sequence
#> [1] "AACTTTATACTTCATCTTCGGAGTTTGATCAGGAATAGTTGGTACATCATTAAGAATTTTAATTCGTGCTGAATTAAGTCAACCAGGTATATTTATTGGAAATGACCAAATTTATAATGTAATTGTTACAGCTCATGCTTTTATTATAATTTTCTTTATAGTTATACCTATTATAATTGGAGGATTTGGAAATTGACTAGTTCCTCTAATATTAGGAGCCCCAGATATAGCTTTCCCTCGAATAAATAATATAAGTTTTTGAATACTACCTCCCTCATTAACTCTTCTACTTTCAAGTAGTATAGTAGAAAATGGGTCAGGAACAGGATGAACAGTTTATCCACCTCTTTCATCTGGAACTGCTCATGCAGGAGCCTCTGTTGATTTAACTATTTTTTCTCTTCATTTAGCCGGAGTTTCATCAATTTTAGGGGCTGTAAATTTTATTACTACTGTAATTAATATACGATCTGCAGGAATTACTCTTGATCGACTACCTTTATTCGTTTGATCTGTAGTAATTACAGCTGTTTTATTACTTCTTTCACTTCCTGTATTAGCTGGAGCTATTACAATACTATTAACTGATCGAAATTTAAATACATCTTTCTTTGACCCAATTGGAGGGGGAGACCCAATTTTATACCAACATTTATTT\r"
And you can search by researcher name
bold_seq(researchers = 'Thibaud Decaens')[[1]]
#> $id
#> [1] "ECHUB386-11"
#>
#> $name
#> [1] "Haplotaxida"
#>
#> $gene
#> [1] "ECHUB386-11"
#>
#> $sequence
#> [1] "AACTCTATACTTTATTTTAGGGGTATGAGCAGGAATAATTGGAGCGGGAATAAGACTCCTAATCCGAATTGAACTAAGACAGCCTGGGGCATTCCTAGGAAGAGATCAATTATATAACACCATTGTTACTGCACATGCATTCCTAATAATCTTCTTCTTGGTAATACCAGTATTTATTGGAGGGTTCGGAAACTGACTCCTACCTCTAATACTGGGTGCGCCCGACATAGCATTTCCACGACTAAACAACATAAGATTTTGACTTCTACCACCATCACTAATTCTTTTAATCTCATCTGCCGCCGTAGAAAAAGGAGCGGGGACAGGATGAACTGTCTATCCCCCGTTAGCAAGAAACATAGCCCACGCAGGTCCATCAGTAGATCTGGCAATTTTCTCACTACATTTAGCCGGAGCCTCATCAATTCTAGGGGCAATTAATTTTATCACCACAGTGGTAAATATACGATGAAGAGGTTTGAAACTGGAACGAGTATCACTTTTCGTGTGAGCGGTAATAATCACAGTAGTATTACTACTACTCTCACTTCCAGTTCTTGCTGGTGCCATTACCATACTATTAACTGACCGAAACCTTAATACATCATTCTTCGACCCCGCAGGAGGCGGAGATCCGATCCTTTATCAACACCTATTC\r"
by taxon IDs
bold_seq(ids = c('ACRJP618-11', 'ACRJP619-11'))
#> [[1]]
#> [[1]]$id
#> [1] "ACRJP618-11"
#>
#> [[1]]$name
#> [1] "Lepidoptera"
#>
#> [[1]]$gene
#> [1] "ACRJP618-11"
#>
#> [[1]]$sequence
#> [1] "------------------------TTGAGCAGGCATAGTAGGAACTTCTCTTAGTCTTATTATTCGAACAGAATTAGGAAATCCAGGATTTTTAATTGGAGATGATCAAATCTACAATACTATTGTTACGGCTCATGCTTTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTTCCCCTTATACTAGGAGCCCCAGATATAGCTTTCCCTCGAATAAACAATATAAGTTTTTGGCTTCTTCCCCCTTCACTATTACTTTTAATTTCCAGAAGAATTGTTGAAAATGGAGCTGGAACTGGATGAACAGTTTATCCCCCACTGTCATCTAATATTGCCCATAGAGGTACATCAGTAGATTTAGCTATTTTTTCTTTACATTTAGCAGGTATTTCCTCTATTTTAGGAGCGATTAATTTTATTACTACAATTATTAATATACGAATTAACAGTATAAATTATGATCAAATACCACTATTTGTGTGATCAGTAGGAATTACTGCTTTACTCTTATTACTTTCTCTTCCAGTATTAGCAGGTGCTATCACTATATTATTAACGGATCGAAATTTAAATACATCATTTTTTGATCCTGCAGGAGGAGGAGATCCAATTTTATATCAACATTTATTT\r"
#>
#>
#> [[2]]
#> [[2]]$id
#> [1] "ACRJP619-11"
#>
#> [[2]]$name
#> [1] "Lepidoptera"
#>
#> [[2]]$gene
#> [1] "ACRJP619-11"
#>
#> [[2]]$sequence
#> [1] "AACTTTATATTTTATTTTTGGTATTTGAGCAGGCATAGTAGGAACTTCTCTTAGTCTTATTATTCGAACAGAATTAGGAAATCCAGGATTTTTAATTGGAGATGATCAAATCTACAATACTATTGTTACGGCTCATGCTTTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTTCCCCTTATACTAGGAGCCCCAGATATAGCTTTCCCTCGAATAAACAATATAAGTTTTTGGCTTCTTCCCCCTTCACTATTACTTTTAATTTCCAGAAGAATTGTTGAAAATGGAGCTGGAACTGGATGAACAGTTTATCCCCCACTGTCATCTAATATTGCCCATAGAGGTACATCAGTAGATTTAGCTATTTTTTCTTTACATTTAGCAGGTATTTCCTCTATTTTAGGAGCGATTAATTTTATTACTACAATTATTAATATACGAATTAACAGTATAAATTATGATCAAATACCACTATTTGTGTGATCAGTAGGAATTACTGCTTTACTCTTATTACTTTCTCTTCCAGTATTAGCAGGTGCTATCACTATATTATTAACGGATCGAAATTTAAATACATCATTTTTTGATCCTGCAGGAGGAGGAGATCCAATTTTATATCAACATTTATTT\r"
by container (containers include project codes and dataset codes)
bold_seq(container = 'ACRJP')[[1]]
#> $id
#> [1] "ACRJP003-09"
#>
#> $name
#> [1] "Lepidoptera"
#>
#> $gene
#> [1] "ACRJP003-09"
#>
#> $sequence
#> [1] "AACATTATATTTTATTTTTGGGATCTGATCTGGAATAGTAGGGACATCTTTAAGTATACTAATTCGAATAGAACTAGGAAATCCTGGATGTTTAATTGGGGATGATCAAATTTATAATACTATTGTTACAGCTCATGCTTTTATTATAATTTTTTTTATAGTTATACCCATTATAATTGGAGGTTTTGGCAATTGACTTGTACCATTAATATTAGGAGCCCCTGATATAGCATTTCCCCGAATAAATAATATAAGATTTTGACTTCTTCCCCCCTCATTAATTTTATTAATTTCAAGAAGAATTGTTGAAAATGGAGCAGGAACAGGATGAACAGTCTATCCTCCATTATCTTCTAATATTGCGCATAGAGGATCCTCTGTTGATTTAGCTATTTTCTCACTTCATTTAGCAGGAATTTCTTCTATTTTAGGAGCAATTAATTTTATTACAACTATTATTAATATACGAATAAATAATTTACTTTTTGACCAAATACCTCTATTTGTTTGAGCAGTAGGTATTACAGCTGTTCTTCTTTTATTATCATTACCAGTATTAGCAGGAGCAATTACCATACTATTAACAGATCGTAATTTAAATACTTCTTTCTTTGATCCTGCTGGAGGAGGAGATCCAATTTTATACCAACATTTATTT\r"
by bin (a bin is a Barcode Index Number)
bold_seq(bin = 'BOLD:AAA5125')[[1]]
#> $id
#> [1] "ASARD6776-12"
#>
#> $name
#> [1] "Lepidoptera"
#>
#> $gene
#> [1] "ASARD6776-12"
#>
#> $sequence
#> [1] "AACTTTATATTTTATTTTTGGAATTTGAGCAGGTATAGTAGGAACTTCTTTAAGATTACTAATTCGAGCAGAATTAGGTACCCCCGGATCTTTAATTGGAGATGACCAAATTTATAATACCATTGTAACAGCTCATGCTTTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGAGGATTTGGAAATTGATTAGTACCCCTAATACTAGGAGCTCCTGATATAGCTTTCCCCCGAATAAATAATATAAGATTTTGACTATTACCCCCATCTTTAACCCTTTTAATTTCTAGAAGAATTGTCGAAAATGGAGCTGGAACTGGATGAACAGTTTATCCCCCCCTTTCATCTAATATTGCTCATGGAGGCTCTTCTGTTGATTTAGCTATTTTTTCCCTTCATCTAGCTGGAATCTCATCAATTTTAGGAGCTATTAATTTTATCACAACAATCATTAATATACGACTAAATAATATAATATTTGACCAAATACCTTTATTTGTATGAGCTGTTGGTATTACAGCATTTCTTTTATTGTTATCTTTACCTGTACTAGCTGGAGCTATTACTATACTTTTAACAGATCGAAACTTAAATACATCATTTTTTGACCCAGCAGGAGGAGGAGATCCTATTCTCTATCAACATTTATTT\r"
And there are more ways to query, check out the docs for ?bold_seq.
Search for specimen data only
The BOLD specimen API doesn’t give back sequences, only specimen data. By default you download tsv format data, which is given back to you as a data.frame
res <- bold_specimens(taxon = 'Osmia')
head(res[,1:8])
#> processid sampleid recordID catalognum fieldnum
#> 1 ASGCB255-13 BIOUG07489-F04 3955532 BIOUG07489-F04
#> 2 BBHYA3298-12 BIOUG02688-A06 2711807 BIOUG02688-A06 L#11BIOBUS-2558
#> 3 BBHYL310-10 10BBCHY-3264 1769753 10BBCHY-3264 L#PC2010KT-025
#> 4 BBHYL365-10 10BBCHY-3319 1769808 10BBCHY-3319 L#PC2010YO-150
#> 5 BCHYM412-13 BC ZSM HYM 18272 3896353 BC ZSM HYM 18272 BC ZSM HYM 18272
#> 6 BCT023-06 06-BCT-023 240799 06-BCT-023
#> institution_storing collection_code
#> 1 Biodiversity Institute of Ontario NA
#> 2 University of Guelph, Centre for Biodiversity Genomics NA
#> 3 University of Guelph, Centre for Biodiversity Genomics NA
#> 4 University of Guelph, Centre for Biodiversity Genomics NA
#> 5 SNSB, Zoologische Staatssammlung Muenchen NA
#> 6 University of Guelph, Centre for Biodiversity Genomics NA
#> bin_uri
#> 1 BOLD:ABZ2181
#> 2 BOLD:ACF5858
#> 3 BOLD:AAC3295
#> 4 BOLD:AAC8510
#> 5 BOLD:AAP2416
#> 6 BOLD:AAB1785
You can optionally get back the data in XML format
bold_specimens(taxon = 'Osmia', format = 'xml')
<?xml version="1.0" encoding="UTF-8"?>
<bold_records xsi:noNamespaceSchemaLocation="http://www.boldsystems.org/schemas/BOLDPublic_record.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
<record>
<record_id>1470124</record_id>
<processid>BOM1525-10</processid>
<bin_uri>BOLD:AAN3337</bin_uri>
<specimen_identifiers>
<sampleid>DHB 1011</sampleid>
<catalognum>DHB 1011</catalognum>
<fieldnum>DHB1011</fieldnum>
<institution_storing>Marjorie Barrick Museum</institution_storing>
</specimen_identifiers>
<taxonomy>
You can choose to get the httr response object back if you’d rather work with the raw data returned from the BOLD API.
res <- bold_specimens(taxon = 'Osmia', format = 'xml', response = TRUE)
res$url
#> [1] "http://v4.boldsystems.org/index.php/API_Public/specimen?taxon=Osmia&format=xml"
res$status_code
#> [1] 200
res$headers
#> NULL
Search for specimen plus sequence data
The specimen/sequence combined API gives back specimen and sequence data. Like the specimen API, this one gives by default tsv format data, which is given back to you as a data.frame. Here, we’re setting sepfasta=TRUE so that the sequence data is given back as a list, and taken out of the data.frame returned so the data.frame is more manageable.
res <- bold_seqspec(taxon = 'Osmia', sepfasta = TRUE)
res$fasta[1:2]
#> $`ASGCB255-13`
#> [1] "-------------------------------GGAATAATTGGTTCTGCTATAAGTATTATTATTCGAATAGAATTAAGAATTCCTGGATCATTCATTTCTAATGATCAAACTTATAATTCTTTAGTAACAGCTCATGCTTTTTTAATAATTTTTTTTCTTGTAATACCATTTTTAATTGGTGGATTTGGAAATTGATTAATTCCATTAATATTAGGAATCCCAGATATAGCATTTCCTCGAATAAATAATATTAGATTTTGACTTTTACCCCCATCCTTAATAATTTTACTTTTAAGAAATTTCTTAAATCCAAGTCCAGGAACAGGTTGAACTGTATATCCCCCCCTTTCTTCTTATTTATTTCATTCTTCCCCTTCTGTTGATTTAGCTATTTTTTCTCTTCATATTTCTGGTTTATCTTCCATCATAGGTTCTTTAAATTTTATTGTTACAATTATTATAATAAAAAATATTTCATTAAAACATATTCAATTACCTTTATTTCCTTGATCCGTTTTTATTACAACTATTTTACTATTATTTTCTTTACCTGTTCTAGCAGGAGCTATTACTATATTATTATTTGATCGAAACTTTAATACTTCATTTTTTGATCCAACTGGAGGAGGAGATCCAATTTTATATCAACATTTATTC"
#>
#> $`BBHYA3298-12`
#> [1] "AATTTTATACATAATTTTTGCTATATGATCAGGAATAATTGGTTCAGCAATAAGTATTATTATTCGTATAGAACTAAGTATTCCTGGTTCATGAATTTCAAATGATCAAACCTATAACTCTTTAGTAACCGCACATGCTTTTTTAATAATTTTTTTTTTAGTAATACCATTTTTAATTGGAGGATTTGGAAATTGATTAGTTCCTTTAATATTAGGAATTCCGGACATAGCTTTTCCACGAATAAATAATATTAGATTTTGACTTTTACCCCCTTCCCTAATAATATTACTTTTAAGAAATTTTCTTAATCCAAGACCTGGAACAGGATGAACTGTATATCCTCCTCTTTCTTCACATTTATTTCATTCTTCTCCTTCAGTTGATATAGCTATTTTTTCTTTACATATTTCTGGTTTATCTTCAATTATAGGATCATTAAATTTTATTGTTACTATTATTATAATAAAAAATATTTCTTTAAAACATATTCAATTACCTTTATTTCCATGATCTGTTTTTATTACTACTATTTTATTACTTTTTTCTTTACCTGTTTTAGCAGGTGCAATTACTATATTATTATTTGATCGAAATTTTAATACTTCATTTTTTGATCCAACAGGAGGAGGAGATCCTATTTTATATCAACATTTATTT"
Or you can index to a specific sequence like
res$fasta['GBAH0293-06']
#> $`GBAH0293-06`
#> [1] "------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTAATGTTAGGGATTCCAGATATAGCTTTTCCACGAATAAATAATATTAGATTTTGACTGTTACCTCCATCTTTAATATTATTACTTTTAAGAAATTTTTTAAATCCAAGTCCTGGAACAGGATGAACAGTTTATCCTCCTTTATCATCAAATTTATTTCATTCTTCTCCTTCAGTTGATTTAGCAATTTTTTCTTTACATATTTCAGGTTTATCTTCTATTATAGGTTCATTAAATTTTATTGTTACAATTATTATAATAAAAAATATTTCTTTAAAATATATTCAATTACCTTTATTTTCTTGATCTGTATTTATTACTACTATTCTTTTATTATTTTCTTTACCTGTATTAGCTGGAGCTATTACTATATTATTATTTGATCGAAATTTTAATACATCTTTTTTTGATCCAACAGGAGGGGGAGATCCAATTCTTTATCAACATTTATTTTGATTTTTTGGTCATCCTGAAGTTTATATTTTAATTTTACCTGGATTTGGATTAATTTCTCAAATTATTTCTAATGAAAGAGGAAAAAAAGAAACTTTTGGAAATATTGGTATAATTTATGCTATATTAAGAATTGGACTTTTAGGTTTTATTGTT---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------"
Get trace files
This function downloads files to your machine - it does not load them into your R session - but prints out where the files are for your information.
bold_trace(taxon='Osmia', quiet=TRUE)
#> Downloading: 51 MB
#> <bold trace files>
#>
#> .../bold/bold_trace_files/BBHYL361-10[LepF1,LepR1]_F.ab1
#> .../bold/bold_trace_files/BBHYL361-10[LepF1,LepR1]_R.ab1
#> .../bold/bold_trace_files/BBHYL363-10[LepF1,LepR1]_F.ab1
#> .../bold/bold_trace_files/BBHYL363-10[LepF1,LepR1]_R.ab1
#> .../bold/bold_trace_files/BBHYL365-10[LepF1,LepR1]_F.ab1
#> .../bold/bold_trace_files/BBHYL365-10[LepF1,LepR1]_R.ab1
#> .../bold/bold_trace_files/FBAPB666-09[LepF1,LepR1]_F.ab1
#> .../bold/bold_trace_files/FBAPB666-09[LepF1,LepR1]_R.ab1
#> .../bold/bold_trace_files/FBAPB667-09[LepF1,LepR1]_R.ab1
Citing
To cite bold in publications use:
Scott Chamberlain (2017). bold: Interface to Bold Systems API. R package version 0.5.0. https://github.com/ropensci/bold
License and bugs
- License: MIT
- Report bugs at our GitHub repo for bold
